Identification of six novel variants from nine Chinese families with hypophosphatemic rickets

Background Hypophosphatemic rickets (HR) is a rare genetic disorder associated with renal phosphate wasting and characterized by bone defects. Inactivating mutations in the phosphate regulating endopeptidase homolog X‑linked gene (PHEX) account for most cases of HR. The aim of this study was to identify causative variants in nine unrelated Chinese families associated with HR, and to determine potential pathogenicity of the identified variants. Methods Genomic DNA was isolated from the peripheral blood of HR patients and their healthy relatives, followed by next-generation sequencing and/or Sanger sequencing. In silico prediction combined with conservation analysis was performed to assess the effects of the variants, and 3D protein modeling was conducted to predict the functional effects on the encoded protein. Results All HR patients recruited in this study displayed bone deformities and tooth agenesis, as well as reduced serum phosphate levels and elevated urine phosphate levels. Nine PHEX variants were identified in eight families, including four novel variants (c.1661_1726del, c.980A > G, c.1078A > T, and c.1017_1051dup). Of the nine identified PHEX variants, five caused a truncated protein, two caused an altered amino acid, and the other two were the canonical splicing variants. Novel variants c.1336G > A and c.1364 T > C in SLC34A3 were also found in one family. Conservation analysis showed that all the amino acids corresponding to the missense variants were highly conserved. In silico analysis and 3D protein structure modeling confirmed the pathogenicity of these variants. Conclusions This study identified four novel variants in PHEX and two novel variants in SLC34A3 in a Chinese cohort with HR. Our findings highlight the dominant role of PHEX in HR, and expand the genotypic and phenotypic spectra of this disorder. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01305-w.

XLHR is the most common inherited HR type [6,7] and accounts for more than 80% of all documented HR cases, with an incidence of 1 in 20,000 live births [8]. This disorder is caused by inactivating mutation in the PHEX gene. The PHEX gene, involved in the etiology of XLHR, encodes a membrane endopeptidase that is abundantly expressed in osteoblasts, odontoblasts, and chondrocytes [9,10]. Levels of FGF23 is well known to be elevated in XLHR patients [3], as well as in a HR mouse model [11], and plays a key role in HR progression [12]. A study of Hyp mice, an animal model of XLHR caused by mutations in the PHEX gene [13], showed that FGF23 acted downstream of PHEX and that a PHEX mutation directly enhanced the secretion of FGF23 by osteoblasts, leading to reduced renal phosphate resorption and disrupted bone phenotypes [14]. Elevated FGF23 levels have been shown to inhibit the transcription of the genes SLC34A1 and SLC34A3, encoding NaPi-IIa and NaPi-IIc, respectively [15]. In addition, suppression of NaPi-IIa and NaPi-IIc results in impaired renal phosphate reabsorption, and thus an accelerated manifestation of the HR phenotype [16].
Although different types of HR share common clinical manifestations, they have distinct causative factors and follow different patterns of inheritance. Therefore, genetic analysis of HR can aid precise diagnosis and direct therapeutic interventions. Prompted by the availability of next-generation sequencing, molecular diagnosis of HR has been performed in many populations including Europeans [17], Turkish [18], Americans [19], Chinese [20][21][22], and Japanese [23]. To date, 623 mutations in PHEX have been found to contribute to the development of XLHR (HGMD Professional, release 2020.04). In the present study, we recruited 17 HR patients from nine Chinese families to further investigate the pathogenic genes. Nine pathogenic variants in PHEX, and two variants in SLC34A3 were identified, which included four novel variants in PHEX and two in SLC34A3. These findings expand the mutational spectra of PHEX and SLC34A3, and provide evidence of the dominant role of PHEX in HR development.

Subjects
Nine unrelated Chinese families with HR were recruited in this study. In total, 56 individuals (27 male and 29 female) were included, 17 of whom had been diagnosed with HR (5 male and 12 female). Data on variables such as sex, age, height, weight, bone phenotypes, dental phenotypes, and available biochemical indicators were collected at their first visit. Height was converted to age-and sex-specific SDS Z-score based on the standard of the Chinese population [24]. Peripheral blood was collected from all probands and their available family members.

DNA/RNA isolation
Genomic DNA was isolated from peripheral blood using the conventional proteinase K-phenol-chloroform method [25]. Total RNA was obtained using Trizol reagent (Invitrogen, CA, USA) from peripheral blood, in accordance with the manufacturer's instructions. Subsequently, cDNA was prepared from 1 µg of RNA using PrimeScript RT reagent kit with gDNA eraser (TaKaRa).

Sanger sequencing and genomic panel sequencing
Sanger sequencing was employed to screen the variants in PHEX. Primers designed for each exon are listed in Additional file 1: Table S1. DNA was amplified using a PCR system (TaKaRa). Sequencing was performed using Applied Biosystems 3739xl DNA analyser (Thermo Fisher Scientific, Waltham, MA, USA). For the probands with no variant identified in PHEX, customized panel sequencing including 184 skeleton-related genes (Additional file 1: Table S2) was conducted as previously described [25]. A total of 1-3 μg genomic DNA was used for panel sequencing. Briefly, DNA samples were sheared into 200 bp fragments using a Bioruptor NGS sonication device (Diagenode, Seraing, Belgium). After purification and library construction, hybridization reactions were performed, followed by sequencing performed on a HiSeq 2500 system (Illumina, San Diego, CA, USA). Sanger sequencing was used to verify the variants in the candidate genes. The sequencing results were analyzed using CodonCode Aligner (version 6.0.2.6; CodonCode, Centerville, MA, USA).

Reverse-transcription PCR (RT-PCR) and amplicon sequencing
RT-PCR was carried out to determine the effects of the variants at the mRNA level. Primers were designed (Additional file 1: Table S1) via the online tool Primer 3 (http:// prime r3. ut. ee/), followed by examination using in silico PCR (http:// genome. ucsc. edu/ cgi-bin/ hgPcr). The PCR products were separated on 2% agarose gel, and separated bands were isolated and processed for amplicon sequencing.

Clinical manifestations
In this study, nine Chinese HR families were recruited, and the pedigrees are presented in Fig. 1A. The clinical symptoms are briefly summarized in Table 1. In general, poor dental development (Fig. 1C, E, F, I, M, P, T) and bone deformities (Fig. 1B, D, G, J, N, O, Q-S, U-X) were present in all HR patients within the recruited families. Notably, most HR patients were experiencing short stature (II-1 (family 1), I-2/II-2 (family 3), II-3 (family 5), III-9 (family 6), as well as II-1 (family 7)) and frequent fractures (family 2, 4 ( Fig. 1K, L), 5, 6, 7 and 9). HR patients in family 1, 2, 3 ( Fig. 1H), and 8 also displayed impaired physical mobility, and bone pain was reported in family 2, 3, and 4. In addition to these common HR characteristics, HR patients in family 5 also displayed knee valgus and scoliosis. The proband II-1 in family 9 showed kyphosis (Fig. 1Y, Z), as well as insensitivity to pain and temperature in the left arm.

Assessment of biochemical indicators in HR patients
Biochemical data were collected and are summarized in Table 2. It was found that the serum phosphate and serum creatinine levels were reduced in all HR patients, while β-CTX and urine phosphate levels were elevated, compared to healthy controls. Normal to high alkaline phosphatase (ALP) levels were found in patients' serum, and very high ALP levels were detected in proband 6 (575.00 U/L), proband 8 (757.90 U/L), and proband 9 (555.00 U/L). Levels of parathyroid hormone (PTH), an important hormone that regulates calcium and phosphorus metabolism, varied between individuals, with elevated levels detected in the majority of the HR patients.

Identification of variants in PHEX and SLC34A3
Sanger sequencing of the exons and associated splicing sites, as well as both UTR regions of the PHEX gene revealed nine PHEX variants in family 1-8 (Table 1, Fig. 2). Among these nine PHEX variants, four were novel (c.1661_1726del, c.980A > G, c.1078A > T, and c.1017_1051dup), and five were previously reported in HGMD (c.591A > G, c.1735G > A, c.1079 + 1G > A, c.1965 + 1G > A, and c.1699C > T). All families carrying PHEX variants exhibited an X-linked dominant inheritance, with the exceptions of family 2, 4, 7, and 8, in which de novo variants were detected. In family 1, although variant c.591A > G (p.Gln197Gln) was supposed to be a synonymous variant, sequencing at the mRNA level identified the deletion of 77 bp at the 3′ region of exon 5 ( Fig. 2A, B). mRNA sequencing was also conducted in family 2 (Fig. 2C). This confirmed that the variant c.1661_1726del did not lead to alternative splicing, but rather to the deletion of 66 bp spanning from 3′ of exon 16 to 5′ of exon 17 (Fig. 2C). A cis double variant c.[980A > G; 1078A > T] was found in family 3 (Fig. 2D), with both variants being inherited from the mother. In family 6, the proband (III-9) with HR (c.1017_1051dup in PHEX) married III-8 with hereditary spastic paraplegia harboring the variant c.715C > T(p. Arg239Cys) in ALT1. Their daughter (IV-1) inherited both variants and exhibited the phenotypes of both diseases.  The pathogenic gene of family 9 was SLC34A3, and proband 9 was a heterozygote of variants c.1336G > A(p. Val446Ile) and c.1364T > C(p.Leu455Pro) ( Table 1). The variant c.1336G > A was inherited from the father, while c.1364 T > C was inherited from the mother. The younger brother of the proband (II-2) inherited neither of these variants from the parents (Fig. 2J, Additional file 1: Fig. S2).

Bioinformatic analysis of the variants
It was confirmed that all point mutation sites, p.Y327C, p.K360*, and p.G579R in PHEX, and p.V446I and p.L455P in SLC34A3, were highly evolutionarily conserved (Fig. 3A). To predict the likelihood of pathogenicity, two online tools (PROVEAN and PolyPhen-2) were used and the predicted scores are summarized in Additional file 1: Table S3. In addition, the splice site variants were predicted as "most probably affecting splicing" by Human Splicing Finder (version 3.1) (Additional file 1: Table S3). The 3D structure of the PHEX protein was modeled by Phyre2 for the deletion c.1661_1726del in PHEX. In comparison to the wild-type PHEX protein, the mutant PHEX protein lacked an α-helix (5′ of exon 17) and a β-sheet (3′ of exon 16) (Fig. 3B), which altered its 3D conformation. The 3D structure of the PHEX protein was also modeled by Swiss-Model and the functional consequences of the missense variants c.980A > G(p.Tyr-327Cys) and c.1735G > A(p.Gly579Arg) were simulated by Pymol (Fig. 3B). This analysis indicated altered interactions of the substituted amino acids with their neighboring residues.
Common consequences of gene mutations are dysfunction of protein, frameshift, truncated protein, protein redundancy, and lack of protein product resulting from mRNA degradation. It has been reported that most cases of XLHR induced by PHEX mutations are caused by the generation of a truncated protein or by the translation of a dysfunctional PHEX product [29], and this was further confirmed in the current study. (i) It has previously been reported that about 85% of PHEX mutations result in a truncated PHEX protein [22]. Three novel variants identified in this study, c.1661_1726del(p. Glu554_Gly575del), c.1078A > T(p.Lys360*), and c.1017_1051dup(p.Phe351Trpfs*16), as well as two previously reported variants c.591A > G(p.Gly196Alafs*16) and c.1699C > T(p.Arg567*), resulted in a truncated PHEX protein and the characteristic HR phenotype. The synonymous variant c.591A > G(p.Gln197Gln) resulted in a frameshift-induced premature termination codon (p.Gly196Alafs*16) (Fig. 2A, B), which was caused by the recognition of an alternative splice donor site "GT" located 3 bp upstream of the mutant site in exon 5. This is in line with findings reported by Liao et al. [30]. (ii) Some PHEX mutations, such as missense mutations and a few splicing mutations, resulted in dysfunction of the PHEX protein. Most of the missense mutations found in PHEX, although located at different sites, affect posttranslational modification of the protein, thus leading to loss of protein function [27]. For example, the reported missense mutation c.1735G > A(p.Gly579Arg) identified in family 4 [31,32] was located at the extracellular C-terminal region, which could affect the secondary structure of the PHEX protein by disrupting disulfide bonds [31]. The predicted 3D structure of the PHEX protein (Fig. 3B) also indicated that Gly579Arg, a change involving substitution of the short-side-chain glycine for the long-sidechain arginase, would possibly push away the interacting α-helix, having a negative effect on protein function. Compared with the severely impacted physical mobility reported in a Turkish family with the same variant [31], the clinical symptoms of the HR patients in this study were limited to mild bone deformities.
The proband in family 3 carried a missense variant c.980A > G(p.Tyr327Cys) and a nonsense variant c.1078A > T(p.Lys360*) (Fig. 2D), both located on the same allele and inherited from his mother (Additional file 1: Fig. S1C). It has previously been shown that a truncated protein generated from a nonsense mutation can cause abnormal bone mineralization and hypophosphatemia [33]. The above-mentioned nonsense variant was therefore predicted to be pathogenic, which was supported by in silico tools (Additional file 1: Table S3). Meanwhile, for the novel missense variant c.980A > G also located in exon 9, there were conflicting results on its pathogenicity (Additional file 1: Table S3). According to Gaucher et al. [17], missense mutations at highly conserved sites encoding residues in the interior of the PHEX protein could alter protein folding and trafficking. The missense variant c.980A > G(p.Tyr327Cys) resulted in an exchanged of tyrosine with cysteine, suggesting a potential role in disulfide bond formation and protein folding [31,34]. In line with this, the predicted 3D protein structure and residue interactions (Fig. 3B) suggested that the wildtype tyrosine closely interacted with glutamine 515 at the neighboring α-helix via a hydrogen bond. However, the mutant cysteine could not form this hydrogen bond and did not interact with the α-helix, potentially changing the stability of the protein. The above findings show that the nonsense variant in family 3 contribute to the development of HR, and indicate a potential role also for the missense variant.
No genotypic and phenotypic correlation was found in this study, which is in line with previous findings [22,35]. Nevertheless, the reported variants were concentrated in exons 18-22 (Fig. 4C), indicating that this extracellular C-terminal region is essential for PHEX protein function [36]. It has been reported that patients with variants at the C-terminal region or truncated proteins exhibited more severe HR phenotypes [35], and variants leading to truncated PHEX proteins generally corresponded to decreased tubular reabsorption of phosphate and 1,25(OH) 2 D [37]. Out of the four novel PHEX variants found in the present study, the first two (located in exon 9) resulted in a truncated PHEX product, the third (located in exon 9) resulted in amino acid alteration, and the fourth (located in exon 17) resulted in a truncated protein. Zhang et al. reported that the missense variants were clustered in exons 15,17,19, and 20 in PHEX [22], while the missense variant identified in this study was located in exon 9. This identifies exon 9 as an important novel player in the progression of HR.
The HR patients included in this study had a significantly shorter stature (ranging from − 4.26 to − 11.10 SD) than previously reported HR patients in Chinese cohort (− 2.70 ± 1.60 SD) [22]. Possible reasons for this are chronical nutritional deficiencies and extended periods of untreated disease progression due to patients' living in remote rural areas with limited access to medical facilities. Noteworthy is that HR patients with a more severe phenotype often had a family history. As the majority of the HR patients recruited in this study also had suffered frequent fractures (Table 1), which can be misdiagnosed as osteogenesis imperfecta, clinical examinations combined with molecular testing are crucial for a precise diagnosis.
In this study, one compound heterozygous variant was found in SLC34A3 in family 9 (Fig. 2J, Table 1). SLC34A3 is expressed in tubule cells and is responsible for the maintenance of phosphate homeostasis [38]. In previous studies, phenotypic heterogeneity was found in patients with SLC34A3 variants: approximately 25% of HHRH patients did not exhibit rickets and half lacked renal calcification [39]. It was also shown that heterozygous carriers presented milder skeletal phenotypes than homozygous ones [40]. Typical HR symptoms were noted in the patient with SLC34A3 variants in this study, while the heterozygous carriers (I-1 and I-2) barely showed any noticeable phenotypes. A study with a large sample size is needed to obtain a comprehensive understanding of the genotype/phenotype correlation in HHRH.